Publications

A single-cell atlas of chromatin accessibility in the human genome
Kai Zhang*, James D. Hocker*, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren

An atlas of gene regulatory elements in adult mouse cerebrum
Yang Eric Li*, Sebastian Preissl*, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Yunjiang Qiu, Olivier B. Poirion, Bin Li, Joshua Chiou, Hanqing Liu, Antonio Pinto-Duarte, Naoki Kubo, Xiaoyu Yang, Rongxin Fang, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Michael Miller, Samantha Kuan, David Gorkin, Kyle J. Gaulton, Yin Shen, Michael Nunn, Eran A. Mukamel, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

Comprehensive analysis of single cell ATAC-seq data with SnapATAC
Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K. Shiau, Xinzhu Zhou, Fangming Xie, Eran A. Mukamel, Kai Zhang, Yanxiao Zhang, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

Cardiac cell type–specific gene regulatory programs and disease risk association
James D. Hocker, Olivier B. Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui-Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang E. Li, Yanxiao Zhang, Elie N. Farah, Allen Wang, Andrew D. McCulloch, Kyle J. Gaulton, Bing Ren^#, Neil C. Chi^#, Sebastian Preissl^#

Single cell multiomic profiling of human lung reveals cell type-specific and age-dynamic control of SARS-CoV2 host genes
Allen Wang*, Joshua Chiou*, Olivier B Poirion*, Justin Buchanan*, Michael J Valdez*, Jamie M Verheyden, Xiaomeng Hou, Parul Kudtarkar, Sharvari Narendra, Jacklyn M Newsome, Minzhe Guo, Dina A Faddah, Kai Zhang, Randee E Young, Justinn Barr, Eniko Sajti, Ravi Misra, Heidie Huyck, Lisa Rogers, Cory Poole, Jeffery A Whitsett, Gloria Pryhuber, Yan Xu, Kyle J Gaulton, Sebastian Preissl, Xin Sun, NHLBI LungMap Consortium

Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium

Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss
Mengchi Wang*, David Wang*, Kai Zhang, Vu Ngo, Shicai Fan, Wei Wang

Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse
Vu Ngo*, Zhao Chen*, Kai Zhang, John W. Whitaker, Mengchi Wang, Wei Wang

Identification of DNA motifs that regulate DNA methylation
Mengchi Wang, Kai Zhang, Vu Ngo, Chengyu Liu, Shicai Fan, John W Whitaker, Yue Chen, Rizi Ai, Zhao Chen, Jun Wang, Lina Zheng, Wei Wang

Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers
Shicai Fan^#, Jianxiong Tang, Nan Li, Ying Zhao, Rizi Ai, Kai Zhang, Mengchi Wang, Wei Du, Wei Wang^#

Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development
Kai Zhang, Mengchi Wang, Ying Zhao, Wei Wang

Bayesian Networks Predict Neuronal Transdifferentiation
Richard I. Ainsworth, Rizi Ai, Bo Ding, Nan Li, Kai Zhang, Wei Wang

Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge
Wei Wei, Zhanglong Ji, Yupeng He, Kai Zhang, Yuanchi Ha, Qi Li, Lucila Ohno-Machado

Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
Bingfei Yu*, Kai Zhang*, J Justin Milner, Clara Toma, Runqiang Chen, James P Scott-Browne, Renata M Pereira, Shane Crotty, John T Chang, Matthew E Pipkin, Wei Wang^#, Ananda W Goldrath^#

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours
J. Justin Milner, Clara Toma, Bingfei Yu, Kai Zhang, Kyla Omilusik, Anthony T. Phan, Dapeng Wang, Adam J. Getzler, Toan Nguyen, Shane Crotty, Wei Wang, Matthew E. Pipkin, Ananda W. Goldrath

Constructing 3D interaction maps from 1D epigenomes
Yun Zhu*, Zhao Chen*, Kai Zhang, Mengchi Wang, David Medovoy, John W. Whitaker, Bo Ding, Nan Li, Lina Zheng, Wei Wang

Systematic identification of protein combinations mediating chromatin looping
Kai Zhang, Nan Li, Richard I. Ainsworth, Wei Wang

Isolation and functional characterization of P-TEFb-associated factors that control general and HIV-1 transcriptional elongation
Ruichuan Chen, Min Liu, Kai Zhang, Qiang Zhou

Signal-induced Brd4 release from chromatin is essential for its role transition from chromatin targeting to transcriptional regulation
Nanping Ai*, Xiangming Hu*, Feng Ding*, Bingfei Yu, Huiping Wang, Xiaodong Lu, Kai Zhang, Yannan Li, Aidong Han, Wen Lin, Runzhong Liu^#, Ruichuan Chen^#